Joubert was the son of an indigent farmer-missionary who trekked his family north to Natal in 1837. When his father died, the family settled on a farm (Rustfontein) in the Transvaal (later South African Republic). With little formal schooling, Joubert educated himself and became a prosperous law and property agent. He began his public career in 1860 as a member of the Volksraad (parliament) and acted as vice president when Pres. Thomas François Burgers visited Europe in 1875–76.

In 1877 the British annexed the South African Republic, designating it the Crown Colony of the Transvaal. Joubert, opposed to the annexation and determined to restore his nation’s independence, worked with Kruger in attempts to negotiate Boer differences with the British by meeting with various officials in Southern Africa and London. After seemingly exhausting peaceful means, the Boer leaders reluctantly proposed and advocated rebellion in December 1880. While Kruger devoted himself to political affairs, Joubert, as commandant general, led his burghers to victory at Laing’s Nek, Ingogo, and Majuba Hill. He took part in negotiating the Pretoria Convention (1881), which restored the independence of the Transvaal.

Joubert’s more progressive views brought him increasingly into conflict with Kruger, who defeated him decisively in the presidential election of 1883. As vice president and, therefore, acting president during Kruger’s absence in London (September 1883 to July 1884), Joubert sought to extend the Transvaal’s borders, but Kruger curbed his efforts. Differences between the two widened as Joubert allied himself with the English-speaking community and objected to the influence of Hollanders in Kruger’s government. Joubert unsuccessfully ran for president against Kruger three more times (1888, 1893, and 1898). He came closest in 1893, winning 7,246 votes to Kruger’s 7,911.

As war approached with Britain (the South African War, 1899–1902), Joubert advocated a policy of conciliation. Once the war began, he became commandant general of the Transvaal’s forces. Though a gallant soldier, Joubert was shortsighted in his preparations, and his extreme caution and inclination to fight a defensive war prevented him from exploiting initial Boer successes.